Substrates having surfaces in a highly clean condition are subjected to a thermal process in a heating furnace. In a thermal processing apparatus for processing substrates by a predetermined thermal process that heats the substrates by a heating means, the substrates are held in a vertical position at horizontal intervals in a reaction vessel. Cleaning liquids are supplied into the reaction vessel to clean the substrates, and then the cleaning liquids are drained away through a drain port, and then a process gas is supplied into the reaction vessel to process the substrates by a thermal process. The substrates having the cleaned clean surfaces are subjected to the thermal process without being exposed to the ambient atmosphere and can be satisfactorily processed by the thermal process.